LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
variable        trequis equal 750.0
variable        prequis_low equal 0.0
variable        prequis_high equal 25.0e4
variable        equilSteps equal 200
variable        runSteps equal 2000
variable        freqdump equal 200
variable        pstime equal step*dt
variable        sxx equal 1.e-4*pxx
variable        syy equal 1.e-4*pyy
variable        szz equal 1.e-4*pzz
variable        sxy equal 1.e-4*pxy
variable        sxz equal 1.e-4*pxz
variable        syz equal 1.e-4*pyz
variable        TK  equal temp
variable        PE  equal pe
variable        KE  equal ke
variable        V   equal vol

dimension       3
boundary        p p p
units           metal
atom_style      atomic
read_data       data.zr_cell
Reading data file ...
  orthogonal box = (0 0 0) to (19.374 33.556752 30.846)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  864 atoms
  read_data CPU = 0.002 seconds
replicate       1 5 5
Replication is creating a 1x5x5 = 25 times larger system...
  orthogonal box = (0 0 0) to (19.374 167.78376 154.23)
  1 by 1 by 1 MPI processor grid
  21600 atoms
  replicate CPU = 0.001 seconds

change_box      all triclinic
Changing box ...
  triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0)

pair_style      hybrid/overlay zero 9.0 eam/fs
pair_coeff * *  zero
pair_coeff * *  eam/fs Zr_mm.eam.fs Zr
Reading eam/fs potential file Zr_mm.eam.fs with DATE: 2007-06-11

timestep        0.002

thermo          50
thermo_style    custom step pe ke temp vol pxx pyy pzz pxy pyz pxz

# fix             extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}"  file thermo_global_npt_low_temperature_Zr_hcp.dat

velocity        all create ${trequis} 42345 dist gaussian
velocity        all create 750 42345 dist gaussian

# 1st step : compute the bispectrum on 24 nearest neighbors
compute         bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25

# 2nd step : perform dimension reduction + logistic regression
compute         slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*]
Files used:
  database mean descriptor: dir.slcsa/mean_descriptor.dat
  lda scalings            : dir.slcsa/lda_scalings.dat
  lr decision             : dir.slcsa/lr_decision.dat
  lr bias                 : dir.slcsa/lr_bias.dat
  maha stats              : dir.slcsa/mahalanobis_file.dat
For class 0  maha threshold = 5.054
  mean B:
      -23.8329
        4.6638
        3.9805
  icov:
        1.1377      0.1077     -0.0171
        0.1077      0.8846     -0.2577
       -0.0171     -0.2577      0.6783
For class 1  maha threshold = 5.234
  mean B:
      -21.2853
       -6.1583
        1.7948
  icov:
        1.7124      0.0341      0.1966
        0.0341      0.6453       0.288
        0.1966       0.288      1.8991
For class 2  maha threshold = 5.036
  mean B:
      -23.1593
        1.3059
       -5.7549
  icov:
        0.7496     -0.0806     -0.1101
       -0.0806      1.1178      0.1667
       -0.1101      0.1667      0.6711
For class 3  maha threshold = 7.994
  mean B:
       68.1971
        0.1604
       -0.0067
  icov:
        0.9663     -0.1846      0.6622
       -0.1846      8.2371      0.9841
        0.6622      0.9841      5.9601

#dump            d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]

# for testing only. in production use dump as shown above
compute max_slcsa all reduce max c_slcsa[*]
compute min_slcsa all reduce min c_slcsa[*]
thermo_style    custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]

#fix            1 all nvt temp ${trequis} ${trequis} 0.100
fix             1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix             1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix             1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix             1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0
fix             1 all npt temp 750 750 0.100 tri 0 0 1.0

run             ${equilSteps}
run             200
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 11
  ghost atom cutoff = 11
  binsize = 5.5, bins = 4 31 29
  3 neighbor lists, perpetual/occasional/extra = 2 1 0
  (1) pair zero, perpetual
      attributes: half, newton on
      pair build: half/bin/newton/tri
      stencil: half/bin/3d/tri
      bin: standard
  (2) pair eam/fs, perpetual, trim from (1)
      attributes: half, newton on, cut 9.6
      pair build: trim
      stencil: none
      bin: none
  (3) compute sna/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 31.9 | 31.9 | 31.9 Mbytes
   Step         PotEng         KinEng          Temp      c_max_slcsa[1] c_max_slcsa[2] c_max_slcsa[3] c_max_slcsa[4] c_max_slcsa[5] c_min_slcsa[1] c_min_slcsa[2] c_min_slcsa[3] c_min_slcsa[4] c_min_slcsa[5]
         0  -143297.23      2093.9174      750            7.6195146      15.787294      1.2169942      111.01919      2              7.6195146      15.787294      1.2169942      111.01919      2            
        50  -142154.08      1007.7164      360.9442       8.8091564      19.23244       4.2093382      113.87959      2              5.0327148      9.6817454      0.02610585     106.71863      2            
       100  -142365.33      1406.6559      503.83647      8.6272189      17.908949      2.9294666      113.75167      2              6.2058895      11.913521      0.033775944    108.66893      2            
       150  -142188.18      1432.0075      512.91691      8.6441961      18.176321      2.9277374      114.27958      2              5.5899425      10.521867      0.014919473    108.14526      2            
       200  -142000.4       1481.7247      530.72462      8.5895692      18.65646       3.1725758      114.55015      2              5.5955774      10.776385      0.061469343    108.35384      2            
Loop time of 36.3759 on 1 procs for 200 steps with 21600 atoms

Performance: 0.950 ns/day, 25.261 hours/ns, 5.498 timesteps/s, 118.760 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.0837     | 9.0837     | 9.0837     |   0.0 | 24.97
Neigh   | 0.52896    | 0.52896    | 0.52896    |   0.0 |  1.45
Comm    | 0.045416   | 0.045416   | 0.045416   |   0.0 |  0.12
Output  | 26.548     | 26.548     | 26.548     |   0.0 | 72.98
Modify  | 0.1493     | 0.1493     | 0.1493     |   0.0 |  0.41
Other   |            | 0.02088    |            |       |  0.06

Nlocal:          21600 ave       21600 max       21600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          36674 ave       36674 max       36674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.61729e+06 ave 2.61729e+06 max 2.61729e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  5.24007e+06 ave 5.24007e+06 max 5.24007e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5240069
Ave neighs/atom = 242.59579
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:43
